Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors

Bacterial diversity using metagenomics of 16s rDNA in water kefir, an innovative source of probiotics for bee nutrition

Water kefir is a sparkling, slightly acidic fermented beverage made from sugar, water, and water kefir grains, which are a mixture of yeast and bacteria. These grains produce a variety of fermentation compounds such as lactic acid, acetaldehyde, acetoin, ethanol and carbon dioxide. In this study, a high-throughput sequencing technique was used to characterize the bacterial composition of the original water kefir from which potential probiotics were obtained. We studied the bacterial diversity of both water kefir grains and beverages. DNA was extracted from three replicate samples of both grains and beverages using the Powerlyzer Microbial Kit. The hypervariable V1-V2 region of the bacterial 16S ribosomal RNA gene was amplified to prepare six DNA libraries. Between 1.4M and 2.4M base-pairs were sequenced for the library. In total, 28721971 raw reads were obtained from all the samples. Estimated species richness was higher in kefir beverage samples compared to grain samples. Moreover, a higher level of microbial alpha diversity was observed in the beverage samples. Particularly, the predominant bacteria in beverages were Anaerocolumna and Ralstonia, while in grains Liquorilactobacillus dominated, with lower levels of Leuconostoc and Oenococcus. Although the bacterial diversity in kefir grains was low because only three genera were the most represented, all of them are LAB bacteria with the potential to serve as probiotics in the artificial feeding of bees.

Kefir Ameliorates Alcohol-Induced Liver Injury Through Modulating Gut Microbiota and Fecal Bile Acid Profile in Mice

SCOPE

Alcoholic liver disease (ALD) is the leading cause of liver-related deaths worldwide. Kefir has been studied for its properties of anti-obesity, rebuilding intestinal homeostasis, and alleviating non-alcoholic fatty liver disease. However, the possible role of kefir in the prevention or treatment of ALD has not been carefully considered. Here, it evaluated the protective effects of kefir supplementation on alcohol-induced liver injury.

METHODS AND RESULTS

C57BL/6J mice are fed to Lieber-DeCarli liquid diet containing alcohol to build ALD mouse model, followed by oral administration with kefir. Results indicate that kefir treatment improves liver pathological changes, decreases the expression levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) and inflammatory markers, and increases antioxidant levels. Kefir supplementation also restores the intestinal barrier and altered microbial composition, indicates as increases of Blautia, Bacteroides, and Parasutterella and decreases in the Firmicutes/Bacteroidetes (F/B) ratio and populations of Psychrobacter, Bacillus, and Monoglobus. Moreover, kefir supplementation decreases the levels of total bile acids (BAs) and primary BAs and increases the secondary/primary BA ratio. Gut microbes play a key role in the conversion of primary to secondary fecal BAs.

CONCLUSION

Kefir can ameliorate ALD through regulating the composition of the gut microbiota.

Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia

Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.

Fermented Beverage Benefits: A Comprehensive Review and Comparison of Kombucha and Kefir Microbiome

Beverage fermentation is an ancient ritual that has been practised for millennia. It was slowly disappearing from households and communities due to the advancement of manufacturing technology and the marketing of soft drinks until the recent revival of the beverage fermentation culture due to an increase in the demand for health drinks amid the COVID-19 pandemic. Kombucha and kefir are two well-known fermented beverages that are renowned for their myriad of health benefits. The starter materials for making these beverages contain micro-organisms that act like microscopic factories producing beneficial nutrients that have antimicrobial and anticancer effects. The materials modulate the gut microbiota and promote positive effects on the gastrointestinal tract. Due to wide variations in the substrates and types of micro-organisms involved in the production of both kombucha and kefir, this paper compiles a compendium of the micro-organisms present and highlights their nutritional roles.

Microbial Communities in Home-Made and Commercial Kefir and Their Hypoglycemic Properties

Kefir is a popular traditional fermented dairy product in many countries. It has a complex and symbiotic culture made up of species of the genera Leuconostoc, Lactococcus, and Acetobacter, as well as Lactobacilluskefiranofaciens and Lentilactobacillus kefiri. Though kefir has been commercialized in some countries, people are still traditionally preparing kefir at the household level. Kefir is known to have many nutritious values, where its consistent microbiota has been identified as the main valuable components of the product. Type 2 diabetes mellitus (T2DM) is a common diet-related disease and has been one of the main concerns in the world’s growing population. Kefir has been shown to have promising activities in T2DM, mostly via hypoglycemic properties. This review aims to explain the microbial composition of commercial and home-made kefir and its possible effects on T2DM. Some studies on animal models and human clinical trials have been reviewed to validate the hypoglycemic properties of kefir. Based on animal and human studies, it has been shown that consumption of kefir reduces blood glucose, improves insulin signaling, controls oxidative stress, and decreases progression of diabetic nephropathy. Moreover, probiotic bacteria such as lactic-acid bacteria and Bifidobacterium spp. and their end-metabolites in turn directly or indirectly help in controlling many gut disorders, which are also the main biomarkers in the T2DM condition and its possible treatment.

Microbial Communities of Artisanal Fermented Milk Products from Russia

Fermented milk products (FMPs) have numerous health properties, making them an important part of our nutrient budget. Based on traditions, history and geography, there are different preferences and recipes for FMP preparation in distinct regions of the world and Russia in particular. A number of dairy products, both widely occurring and region-specific, were sampled in the households and local markets of the Caucasus republics, Buryatia, Altai, and the Far East and European regions of Russia. The examined FMPs were produced from cow, camel, mare’s or mixed milk, in the traditional way, without adding commercial starter cultures. Lactate and acetate were the major volatile fatty acids (VFA) of the studied FMPs, while succinate, formate, propionate and n-butyrate were present in lower concentrations. Bacterial communities analyzed by 16S rRNA gene V4 fragment amplicon sequencing showed that Firmicutes (Lactococcus, Lactobacillus, Streptococcus, Lentilactobacillus and Leuconostoc) was the predominant phylum in all analyzed FMPs, followed by Proteobacteria (Acetobacter, Klebsiella, Pseudomonas and Citrobacter). Lactobacillus (mainly in beverages) or Lactococcus (mainly in creamy and solid products) were the most abundant community-forming genera in FMPs where raw milk was used and fermentation took place at (or below) room temperature. In turn, representatives of Streptococcus genus dominated the FMPs made from melted or pasteurized milk and fermented at elevated temperatures (such as ryazhenka, cottage cheese and matsoni-like products). It was revealed that the microbial diversity of koumiss, shubat, ryazhenka, matsoni-like products, chegen, sour cream and bryndza varied slightly within each type and correlated well with the same products from other regions and countries. On the other hand, the microbiomes of kefir, prostokvasha, ayran, cottage cheese and suluguni-like cheese were more variable and were shaped by the influence of particular factors linked with regional differences and traditions expressed in specificities in the production process. The microbial diversity of aarts, khurunga, khuruud, tan, ayran and suluguni-like cheese was studied here, to our knowledge, for the first time. The results of this study emphasize the overall similarity of the microbial communities of various FMPs on the one hand, and specificities of regional products on the other. The latter are of particular value in the age of globalization when people have begun searching for new and unusual products and properties. Speaking more specifically, these novel products, with their characteristic communities, might be used for the development of novel microbial associations (i.e., starters) to produce novel products with improved or unique properties.

Volatile Composition and Sensory Profile of Lactose-Free Kefir, and Its Acceptability by Elderly Consumers

Lactose-free products are crucial in the diet of lactose-intolerant elderly consumers, one of them being kefir due to its unique chemical composition and diversity of valuable microflora. The study aimed at determining the volatile compound profile and the corresponding sensory attributes of lactose-free kefir (LFK) as compared with the traditional one (TK). The perception of main sensory attributes and hedonic acceptability of LFK by elderly were also studied. The LFK contained two times more ketones, especially 3-hydroxy-2-butanone and 2,3-butanedione, that probably contributed to the high intensity of creamy aroma. A substantial share of acetic acid in LFK was not associated with high intensity of sour aroma, probably being masked by the creamy aroma, perceived as dominating. LFK was sensed as sweeter and more milky than the traditional one. The intense sweet taste of LFK was due to higher amounts of glucose and galactose than in TK, and was perceived as “just about right” by 63% of elderly subjects in the just-about-right (JAR) scale. The lower acidity of LFK than that of TK, assayed both instrumentally and by sensory assessment, was highly appreciated by 73% of elderly subjects as “just about right” in JAR scale. These two taste attributes dominated in liking the lactose-free kefir by elderly subjects.